Beginnings of Translation: Review of How Amino Acids and Peptides Shaped the RNA World

Molecules have been moving around and stretching in cramped spaces since the beginning of life on this planet.  I just recently read a review paper by van der Gulik and Speijer, two researchers from the Netherlands about this topic. They described how the world may have developed the ability to create proteins from RNA and small peptides.  RNA, as you may know, carry the molecular plans for the cell to build the proteins that more or less make up our cells’ structures.  They do this by working together with another protein structure called a Ribosome to assemble amino acids, the building blocks of proteins.  The plan RNA, called mRNA for “messenger” RNA has to get threaded through a tiny inner cavity in the ribosome. There mRNA meets up with a “transfer” RNA or tRNA carrying an amino acid.  The mRNA and tRNA can then move and stretch to hook amino acids together to construct proteins!  If you look at this process it seems pretty miraculous.  How can all of these molecules can fit together in the proper positions at exactly the right time?   Van der Guilk and Speijer have attempted to piece together a timeline of event to answer this question.

Though it may seem irreducibly complex, this process of protein production could have evolved over time from much simpler reactions in a similarly small space.  To start, van der Guilk and Speijer not how certain types of RNA are known to be able to react with themselves.  They can into a certain position and cut themselves like an enzyme.  For this reason they are often called “Ribozymes”.  Many people studying the early biochemistry of the Earth believe that “life” existed first in the form of an RNA-world of Ribozymes making and cutting other RNAs.  The question then becomes when did proteins come into the mix?  Some believe that Ribozymes eventually gained the ability to form RNA-Ribosomes on their own to assemble proteins.  This is where van der Guilk and Speijer begin to diverge from some of the big names in the field.  These two suggest that the process of going from RNAàProtein occurred with the help of small proteins, peptides, of two-five amino acids.

The central argument of van der Guilk and Speijer comes from two facts, 1: that early peptides could have assembled on their own and 2: that these peptides can stabilize RNA.  Recall that we talked about in my previous post how molecular crowding can change the surroundings of a molecule and force it to stretch or react with other molecules.  In our author’s minds, the RNAàProtein process developed not in the inner cavity of a Ribosome, but in the confined space of montmorillonite, which is like clay from a river or cave.  The low water content conditions inside the layers of clay could have been enough to force two glycine amino acids to come together to form a peptide bond.  These small peptides, the authors argue, could have been the first component of the “ribosome” that might have allowed RNA and Ribozymes to function.  These proteins may have been able to wrap around RNA in a manner that protected it from wrapping around ions like Magnesium (as Mg2+) and cleaving itself.  A peptide scaffold could have then developed specific amino acid side groups like carboxylic acid (COO- when ionized) to further protect RNA.  Hypothetically functional ribosomes could have evolved from these very simple components.

Week3

I’ll leave out the rest of the paper for now which describes higher-order RNA structures and how codons might have developed.  For this, I’ll leave you with the reference to the paper in case you are interested in looking more into it.  Thanks for reading and please leave comment for discussion if you like!

Reference:

Van der Guilk PTS and Speijer D, Life 2015, 5, 230-246.

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